Supporting data for "Comparative transcriptomics of five high-altitude vertebrates and their low-altitude relatives"

Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that examined high-altitude adaptation identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. We generated a total of 910 Gb high-quality RNA-seq data for 180 samples derived from six tissues of five agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat and yak), and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ~75% reads could be aligned to their respective reference genomes, and on average ~70% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.1. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression-based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression, and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes were potentially involved in phenotypic divergence shaped by high-altitude adaptation. This data serves as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments.